Detection of Extracellular Tumor-Associated Nucleic Acid in Blood Plasma or Serum

ABSTRACT

This invention relates to detection of specific extracellular DNA in plasma or serum fractions of human or animal blood associated with neoplastic, pre-malignant or proliferative disease. Specifically, the invention relates to detection tumor-associated DNA, and to those methods of detecting and monitoring tumor-associated DNA found in the plasma or serum fraction of blood by using DNA extraction and amplification with or without enrichment for DNA. The invention allows the selection and monitoring of patients for various cancer therapies including receptor tyrosine kinase inhibitor therapies.

This application is a continuation-in-part of U.S. Ser. No. 11/695,421 filed Apr. 2, 2007, which is a continuation of U.S. Ser. No. 10/680,060, filed Oct. 7, 2003, which is a continuation of U.S. Ser. No. 09/456,222, filed Dec. 7, 1999, now U.S. Pat. No. 6,630,301, issued Oct. 7, 2003, which is a continuation-in-part of U.S. patent application Ser. No. 09/049,234, filed Mar. 27, 1998, now abandoned, which is a continuation-in-part of U.S. patent application Ser. No. 08/818,058, filed Mar. 14, 1997, now U.S. Pat. No. 6,156,504, issued Dec. 5, 2000, which claims priority to U.S. Provisional Application Ser. No. 60/028,180, filed Oct. 15, 1996, and U.S. Provisional Application Ser. No. 60/026,252, filed Sep. 17, 1996, and U.S. Provisional Application Ser. No. 60/013,497, filed Mar. 15, 1996, the entire disclosure of which is hereby incorporated by reference.

BACKGROUND OF THE INVENTION

1. Field of the Invention

This invention relates to methods for detecting specific extracellular nucleic acid in plasma or serum fractions of human or animal blood associated with neoplastic, pre-malignant or proliferative disease. Specifically, the invention relates to detection of nucleic acid derived from mutant oncogenes or other tumor-associated DNA including non-mutated tumor-associated DNA, and to methods of detecting and monitoring extracellular tumor-associated DNA found in the plasma or serum fraction or non-cellular fraction of blood. Methods may optionally include use of DNA enrichment methods, wherein enrichment-based extraction methods are used prior to amplification and/or detection, or wherein enrichment for the nucleic acid of interest occurs during amplification, in particular through use of a restriction endonuclease. The invention permits the detection of extracellular, tumor-associated nucleic acid in the serum or plasma of humans or other animals having a malignant disease or a pre-malignant or proliferative disease or condition, and is further useful in individuals without a prior diagnosis of neoplastic, pre-malignant or proliferative disease or condition in whom the disease or condition is unrecognized. The invention provides the ability to detect extracellular nucleic acid associated with neoplasia, including but not limited to mutated oncogenes and hypermethylated DNA. The invention thereby provides methods for identification and monitoring of neoplasms and premalignant conditions including but not limited to those of the colon, rectum, pancreas, lung, breast, bladder, ovary, cervix, endometrium, liver, prostate, esophagus, head and neck, and stomach. Methods are thereby further provided for the selection of patients for therapies, monitoring of therapies, and monitoring for tumor recurrence. The invention particularly provides methods for detecting tumor-associated DNA associated with the tyrosine kinase pathway, thereby allowing patient selection for and monitoring of therapies directed toward interfering with the tyrosine kinase pathway and tyrosine kinase receptors, including but not limited to tyrosine kinase inhibitors.

2. Description of the Related Art

Neoplastic disease, including most particularly that collection of diseases known as cancer, is a significant part of morbidity and mortality in adults in the developed world, being surpassed only by cardiovascular disease as the primary cause of adult death. Although improvements in cancer treatment have increased survival times from diagnosis to death, success rates of cancer treatment are more closely related to early detection of neoplastic disease that enable aggressive treatment regimes to be instituted before either primary tumor expansion or metastatic growth can ensue. A particular favorable prognosis is achieved if premalignant tissue can be eradicated prior to progression to cancer.

The art recognizes a wide range of DNA alterations associated with cancer and other neoplastic diseases. Such alterations including mutated DNA, such as point mutations, insertions, deletions, and other mutations of oncogenes and tumor suppression genes, translocations, microsatellite alterations, and non-mutated DNA alterations including hypermethylation, hypomethylation, and excess gene copy number. Oncogenes are normal components of every human and animal cell, responsible for the production of a great number and variety of proteins that control cell proliferation, growth regulation, and cell death.

Acquired mutated oncogenes are markers of malignant or premalignant conditions. It is also known that other, non-oncogenic portions of the genome may be altered in the neoplastic state. Nucleic acid based assays as described in the present invention can detect both oncogenic and non-oncogenic DNA, whether mutated or non-mutated.

One group of tumor-associated DNA of particular interest to which the present invention applies are receptor tyrosine kinase-associated DNA, including but not limited to HER-2/neu DNA, epidermal growth factor receptor (EGFR) DNA, c-Kit DNA, and FMS-like tyrosine kinase 3 (Flt3) DNA.

In particular, nucleic acid amplification methods (for example, the polymerase chain reaction) allow the detection of small numbers of mutant molecules among a background of normal ones. While alternate means of detecting small numbers of tumor cells (such as flow cytometry) have generally been limited to hematological malignancies (Dressler and Bartow, 1989, Semin. Diag. Pathol. 6: 55-82), nucleic acid amplification assays have proven both sensitive and specific in identifying malignant cells and for predicting prognosis following chemotherapy (Fey et al., 1991, Eur. J. Cancer 27: 89-94).

Various nucleic acid amplification strategies for detecting small numbers of mutant molecules in solid tumor tissue have been developed, particularly for the ras oncogene (Chen and Viola, 1991, Anal. Biochem. 195: 51-56; Kahn et al., 1991, Oncogene 6: 1079-1083; Pellegata et al., 1992, Anticancer Res. 12: 1731-1736; Stork et al., 1991, Oncogene 6: 857-862). For example, one sensitive and specific method identifies mutant ras oncogene DNA on the basis of failure to cleave a restriction site at the crucial 12th codon (Kahn et al., 1991, ibid.). Similar protocols can be applied to detect any mutated region of DNA in a neoplasm, allowing detection of other oncogene DNA or tumor-associated DNA. Since mutated DNA can be detected not only in the primary cancer but in both precursor lesions and metastatic sites (Dix et al., 1995, Diagn. Molec. Pathol. 4: 261-265; Oudejans et al., 1991, Int. J. Cancer 49: 875-879), nucleic acid amplification assays provide a means of detecting and monitoring cancer both early and late in the course of disease.

While direct analysis of neoplastic tissue is frequently difficult or impossible (such as in instances of occult, unrecognized disease), peripheral blood is easily accessible and amenable to nucleic acid-based assays such as those mentioned above. Many studies have used nucleic acid amplification assays to analyze the peripheral blood of patients with cancer in order to detect intracellular DNA extracted from circulating cancer cells in patients, including one study which detected the intracellular ras oncogene from circulating pancreatic cancer cells (Tada et al., 1993, Cancer Res. 53: 2472-4). However, it must be emphasized that these studies attempt to use nucleic acid-based amplification assays to detect extracted intracellular DNA within circulating cancer cells. The assay is performed on the cellular fraction of the blood from patients having cancer using the cell pellet or cells within whole blood, and the serum or plasma fraction is ignored or discarded prior to analysis. Since such an approach requires the presence of metastatic circulating cancer cells (for non-hematologic tumors), it is of limited clinical use in patients with early cancers, and it is not useful in the detection of non-hematologic non-invasive neoplasms or pre-malignant states. The prior art contains disclosure that mutant oncogene DNA could be detected in peripheral blood plasma or serum of cancer patients (see, for example, Sorenson et al., 1994, Cancer Epidemiology, Biomarkers & Prevention 3: 67-71; Vasioukhin et al., 1994, Br. J. Haematol. 86: 774-9; Vasyukhin et al., in Verna & Shamoo (eds), Biotechnology Today, Ares-Serono Symposia Publications, pp. 141-150). Mutant ras oncogenes have been demonstrated in plasma or serum using polymerase chain reaction. However, these reports have also been generally limited to patients with advanced cancer or known disease.

We have recognized that nucleic acid amplification assays can detect tumor-associated extracellular mutated DNA, including oncogene DNA, in the plasma or serum fraction of blood of humans without cancer or known disease (see U.S. Ser. No. 08/818,058, now U.S. Pat. No. 6,156,504, issued Dec. 5, 2000, incorporated by reference), and that this can be accomplished in a clinically useful manner.

SUMMARY OF THE INVENTION

The present invention provides methods that permit the extraction of nucleic acid from blood plasma or serum of a human or an animal, coupled with detection methods that permit identification of tumor-related DNA, including DNA derived from mutated oncogenes such as mutated K-ras, P53, and APC, and non-mutated tumor-associated DNA. The invention enables detection of tumor-associated DNA in humans without cancer, and thereby determines the presence of premalignant tissue in the human, including premalignant mutated tissue associated with premalignant diseases and conditions such as adenoma, cervical dysplasia, atypical squamous metaplasia of the lung, bronchial dysplasia, atypical hyperplasia of the breast, prostatic intraepithelial neoplasia, atypical endometrial hyperplasia, dysplastic nevi of the skin, and Barrett's esophagus, and therefore provides a predictive risk factor for neoplastic disease, including both malignant, premalignant, precancerous, and non-invasive non-hematologic diseases.

In particular, the present invention enables detection of receptor tyrosine kinase-associated DNA in humans and animals, and thereby facilitates the selection and monitoring of patients with cancer for tyrosine kinase receptor inhibitors or therapeutic agents whose mechanism of action interferes with a tyrosine kinase pathway.

The present invention relates to detection of specific extracellular nucleic acid in plasma or serum in human or animals with or without cancer which are associated with neoplastic, preneoplastic or proliferative disease or conditions. Specifically, the invention relates to the detection of tumor-associated DNA species that are receptor tyrosine kinase DNA or associated with a tyrosine kinase pathway. The invention further encompasses detection of malignant and/or premalignant disease by the direct enrichment of mutated nucleic acid or tumor-associated nucleic acid found in the plasma or serum fraction of blood with respect to wild-type or non-mutated nucleic acid either prior to or during amplification and detection of the nucleic acid, whereby the concentration of the mutant nucleic acid is increased or the mutant nucleic acid is isolated from the remaining non-mutated nucleic acid. The invention thus provides methods for detecting predictive risk markers for a variety of cancers, including colorectal, pancreatic, lung, prostate, esophageal, gastric, breast, bladder, ovarian, cervical, liver, lymphoma, leukemia, and kidney cancer, and other malignancies and premalignant conditions carrying tumor-associated mutations in DNA, as well as methods for monitoring neoplastic disorders in humans and animals. The invention provides as examples but not limitation detection of mutated K-ras, APC, and P53 DNA in plasma or serum. Premalignant diseases or conditions include but are not limited to colorectal adenoma, cervical dysplasia, atypical squamous metaplasia of the lung, bronchial dysplasia, atypical hyperplasia of the breast, prostatic intraepithelial neoplasia, atypical endometrial hyperplasia, dysplastic nevi of the skin, and Barrett's esophagus.

The prior art provides instruction in identifying tumor-associated DNA in the plasma or serum fraction of blood of humans with known malignancy using DNA extraction methods, followed by amplification of the target DNA, followed by detection of the amplified target nucleic acid (see, for example, Sorenson et al., 1993, American Association for Cancer Research Abstract #174; Vasyukhin et al., 1994, Biotechnology Today (Verna & Shamoo, eds.), Ares-Serono Symposia Publications, pp. 141-150; Vasioukhin et al., 1994, Br. J. Haematol. 86: 774-9; Lefort et al., 1995, American Association for Cancer Research Abstract #557; Nawroz et al., 1996, Nature Med. 2:1035-7; Chen et al., 1996, Nature Med. 2: 1033-5). However, the prior art does not apply these methods to non-hematologic premalignancy, or to patients without known disease, or to detection of non-mutated tumor-associated DNA. The methods disclosed herein, in contrast, allow detection of mutant DNA or tumor-associated DNA from the blood of humans without cancer or known disease by providing for the enrichment of mutated nucleic acid, wherein the mutated nucleic acid is concentrated and/or isolated from the remaining extracted nucleic acid prior to or independent of amplification of the target nucleic acid, and thereby provides methods which enable enhanced detection of the target nucleic acid or its fragments. The methods disclosed herein further provide for the enrichment of mutated nucleic acid with respect to wild-type nucleic acid during amplification of the target nucleic acid, and thereby provide for methods which enable the enhanced detection of the target nucleic acid or its fragments. The methods disclosed herein further provide for the detection of extracellular tumor-associated DNA that is a receptor tyrosine kinase DNA.

Extracellular DNA is known to circulate in the serum or plasma fraction of blood (Stroun et al., 1987, Eur. J. Cancer Clin. Oncol. 23: 707-12; Stroun et al., 1989, Oncology 46: 318-322; U.S. Pat. No. 5,496,699 by Sorenson; U.S. Pat. No. 5,952,170 by Stroun et al). The invention disclosed in co-owned U.S. Ser. No. 08/818,058, now U.S. Pat. No. 6,156,504 (incorporated by reference in its entirety), taught methods for identifying mutated extracellular DNA for identification of malignant or premalignant lesions. These methods are useful for diagnosis and treatment of people who have or who are at risk to develop malignancy or premalignancy. Appropriate therapy, including but not limited to, increased surveillance, surgical excision, chemotherapy and immunotherapy or chemoprevention therapies, as well as more innovative therapies (such as antisense oligonucleotide therapy, cancer vaccine therapy, antiangiogenic inhibitor therapy, or treatment with monoclonal antibodies, for example), may be instituted based on detection of mutant or non-mutated tumor-associated nucleic acid in such patients.

Prior to the instant invention and co-owned and co-pending U.S. Ser. No. 08/818,058, now U.S. Pat. No. 6,156,504, it was not known that extracellular mutant nucleic acid could be detected in the blood of humans without cancer. The present invention and co-owned U.S. Ser. No. 08/818,058, now U.S. Pat. No. 6,156,504, teach that detection of extracellular mutant nucleic acid in the blood of humans without cancer can be enhanced by enrichment of the mutated nucleic acid relative to wild-type nucleic acid wherein the mutated nucleic acid is concentrated and/or isolated from the remaining extracted nucleic acid in a manner performed either concurrently or sequentially with the extraction and prior to amplification and/or detection of the target nucleic acid or its fragment. Similarly the methods can be applied to patients and animals with known cancer, or with suspected cancer. Although extracellular mutant tumor-associated DNA has been detected in patients with advanced malignancies (Sorenson et al., 1993, Id.; Vasioukhin et al., 1994, Id.; Nawroz et al., 1996, Id.), it had been presumed in the prior art that only malignancies, and in particular large malignancies, produced enough extracellular DNA to be identified even with prior amplification of the DNA. Co-owned U.S. Ser. No. 08/818,058, now U.S. Pat. No. 6,156,504 (incorporated by reference), taught that mutated oncogenes and other tumor-associated nucleic acid was also detectable in blood serum or plasma of individuals with pre-malignant lesions, diseases, or conditions following amplification of nucleic acid sequences found in blood plasma or serum, as well as in those with malignancies. In the present invention it is further clarified that the methods of the invention can be used for selection and monitoring of receptor tyrosine kinase-directed treatment regimens.

The present invention provides methods for detecting the presence of extracellular nucleic acid in blood plasma or serum fractions, said nucleic acid being associated with a neoplastic, pre-malignant or proliferative disease state in an animal or a human without cancer. The invention provides methods for extracting and enriching extracellular nucleic acid associated with a neoplastic, pre-malignant or proliferative disease state in an animal or a human prior to nucleic acid amplification or signal detection. The invention further provides for methods whereby mutated nucleic acid is enriched with respect to wild-type nucleic acid during or prior to an amplification step wherein a restriction endonuclease is used during or prior to the amplification step. These methods of the invention are used for the detecting, monitoring, evaluating, or risk assessment of premalignant conditions, and in particular those conditions including but not limited to colorectal adenoma, cervical dysplasia, atypical squamous metaplasia of the lung, bronchial dysplasia, atypical hyperplasia of the breast, prostatic intraepithelial neoplasia, atypical endometrial hyperplasia, dysplastic nevi of the skin, and Barrett's esophagus.

In a first aspect, the invention provides a method for detecting extracellular tumor-derived or tumor-associated mutated nucleic acid in a plasma or serum fraction of a blood sample from a human or animal with or without cancer, thereby providing a method for diagnosis, detection, monitoring, evaluation or selection for treatment of a neoplastic or proliferative disease in an animal or a human. The method provided by the invention comprises the steps of: first, purifying extracellular nucleic acid from blood plasma or serum to prepare a preparation of extracted nucleic acid containing a tumor-associated DNA or its fragment; second, optionally enriching for the tumor-associated DNA, either concurrent with or sequentially following the initial extraction step, wherein the tumor-associated DNA or its fragment is concentrated and/or isolated from the remaining extracted nucleic acid; third, amplifying the tumor-associated DNA or its fragment, or amplifying a signal corresponding to the tumor-associated DNA or its fragment; and fourth, detecting the product of the amplified tumor-associated DNA or its fragment, or the amplified signal corresponding to the extracted tumor-associated DNA or its fragment, wherein the DNA or its fragment is associated with neoplastic, pre-malignant or proliferative disease. In preferred embodiments of the invention, the tumor-associated DNA is nucleic acid encoding a mutated oncogene or other tumor-associated DNA, such as a DNA microsatellite alteration or hypermethlyated DNA. In a particularly preferred embodiment of this aspect of the invention, the tumor-associated DNA is receptor tyrosine kinase-related DNA. In one aspect of this embodiment, the tumor-associated DNA is receptor tyrosine kinase DNA selected from the group including but not limited to HER-2/neu DNA, epidermal growth factor receptor (EGFR) DNA, c-kit DNA, c-Met DNA, Flt-3 DNA, and platelet-derived growth factor receptors (PDGFR) DNA.

In another aspect, the invention provides methods for detecting tumor-associated DNA that is DNA associated with a myeloproliferative disease, for example mutated JAK-2 DNA, a DNA associated with polycythemia vera, essential thrombocythemia, and idiopathic myelofibrosis. In one aspect, the invention provides methods for detecting tumor-associated DNA that is JAK-2 V617F mutated DNA.

In a particularly preferred aspect, the invention provides methods for detecting tumor-associated DNA that is translocated DNA including inversions and fusion gene DNA, wherein said tumor-associated DNA include but are not limited to bcl-2/IgH DNA, bcr-ab1 DNA, PML/RAR DNA, AML1-ETO DNA, EWS/FLI-1 DNA, EWS/ERG DNA, ETS family gene fusion DNA, TMPRSS2/ERG DNA, TMPRSS2-ETV1 DNA, TEL-AML1, TMPRSS2-ETV4 DNA, C15orf21/ETS DNA, HNRPA2B1/ETS DNA, RET fusion gene DNA, NTRK1 fusion gene DNA, PAX8-PPARG DNA, MECT1-MAML2 DNA, ETV6-NTRK3 DNA, NPM-ALK DNA, EML4-ALK DNA, TPM3-ALK DNA, TFG-ALK DNA, ATIC-ALK DNA, PAX3-FKHR DNA, PAX7-FKHR DNA, ETV6-PDGFRB DNA, EWSR1-DDIT3 DNA, FUS-DDIT3 DNA, PCM1-JAK2 DNA, BCR-JAK2 DNA SS18-SSX DNA and JAZF1-JJAZ1 DNA.

In another aspect, the invention provides methods for detecting tumor-associated DNA that is a hormone receptor DNA, including but not limited to estrogen receptor DNA, progesterone receptor RNA, insulin and insulin-like growth factor-1 receptor DNA including IGF-I DNA and IGFR-1 DNA, and guanylyl cyclase C (GCC) receptor DNA.

In another aspect, the invention provides a method for detecting extracellular tumor-derived or tumor-associated nucleic acid in a plasma or serum fraction of a blood sample from a human or animal with or without cancer, thereby providing a method for detection, diagnosis, monitoring, evaluation, or treatment of a neoplastic or proliferative disease or premalignant conditions in an animal or a human. The method provided by the invention comprises the steps of: first, purifying extracellular DNA from plasma or serum to prepare a preparation of extracted DNA containing a tumor-associated DNA or its fragment; second, enriching the mutated nucleic acid relative to wild-type nucleic acid using an endonuclease prior to or during amplification; third, amplifying the enriched DNA or its fragment; and fourth, detecting the amplified fragment of the enriched DNA or a signal corresponding to the amplified fragment of the enriched DNA. In preferred embodiments of this aspect of the invention, the nucleic acid is derived from a nucleic acid encoding an oncogene or other tumor-associated DNA. In one aspect of this embodiment, the tumor-associated DNA is receptor tyrosine kinase DNA that is HER-2/neu DNA, EGFR DNA, c-kit DNA, Flt-3 DNA, and/or JAK-2 DNA.

One aspect of this embodiment of the invention comprises detection of nucleic acid sequences derived from or related to mutated p53, K-ras, and APC alleles.

Another aspect of this embodiment of the invention comprises detection of non-mutated DNA.

Another aspect of this embodiment of the invention comprises detection of hypermethylated DNA.

Another aspect of this embodiment of the invention comprises detection of translocated DNA or a fusion gene DNA.

Another aspect of this embodiment of the invention comprises detection of JAK-2 DNA.

In preferred embodiments of the inventive methods, extracellular nucleic acid is extracted from blood plasma or serum using an extraction method including gelatin extraction; silica, glass bead, or diatom extraction; guanidine- or guanidinium-based extraction; chemical extraction methods; and size-exclusion and anion-exchange chromatographic methods. In particularly preferred embodiments, the target DNA is extracted in an enriching manner, or extracted DNA is further enriched, using probe-specific hybridization wherein said hybridizing probes are immobilized to a substrate, wherein such substrate includes but is not limited to nylon and magnetic beads, from which contaminating species (nucleic acid and otherwise) can be removed using methods (such as washing at defined stringencies of salt concentration and temperature) known in the prior art, or wherein alternatively the target DNA of interest may be otherwise isolated from contaminating species including wild-type DNA, for example by application of a magnetic field or an electric field. In preferred embodiments, the extracted and enriched nucleic acid is amplified or signal amplified, wherein the amplification method may include but is not limited to polymerase chain reaction, ligase chain reaction, boomerang DNA amplification, strand displacement amplification, strand displacement activation, cycling probe amplification, and branched DNA signal amplification. In preferred embodiments, DNA detection is performed using a detection method including gel electrophoresis; immunological detection methods; hybridization using a specific, fluorescent-, radioisotope-, antigenic- or chromogenically-labeled probe; Southern blot analysis; electrochemiluminescence; reverse dot blot detection; spectroscopy, mass spectroscopy, and high-performance liquid chromatography.

In a preferred embodiment, the nucleic acid is extracted from blood serum or plasma by heating the serum or plasma, at a temperature from about 90° C. to about 100° C., more preferably from about 95° C. to about 100° C., for a time from about 1 minute to about 20 minutes, more preferably from about 5 minutes to about 15 minutes, and most preferably from about 5 minutes to about 10 minutes. Optionally, the blood plasma or serum can be frozen after boiling to a temperature of from about −20° C. to about 0° C. for at least about 5 minutes, more preferably 15 minutes and most preferably for at least about 30 minutes. The boiled blood plasma or serum is used after cooling or, if frozen, after being thawed to a liquid.

The methods of the invention are provided as methods for detecting tumor-associated extracellular nucleic acid, for example a mutated oncogene, in a human with or without cancer, whereby detection is indicative of the presence of non-hemopoietic cells or tissue containing tumor-associated DNA within the human, comprising the steps of purifying extracellular nucleic acid from a plasma or serum fraction of a blood sample from the human to prepare extracted nucleic acid containing a tumor-associated DNA, for example a mutated oncogene DNA, or its fragment, and concurrently or sequentially; enriching for the tumor-associated DNA or its fragment, wherein the tumor-associated DNA or its fragment is concentrated and/or isolated from the remaining extracted nucleic acid; and amplifying or signal amplifying the tumor-associated DNA or its fragment; and detecting the product of the amplified tumor-associated DNA or its fragment or the amplified signal of the tumor-associated DNA or its fragment. The detected DNA or its fragment is then identified, e.g., as comprising the mutated form of an oncogene associated with a neoplastic, pre-malignant or proliferative disease, wherein detection of the amplified product or the amplified signal or the tumor-associated DNA or its fragment is indicative of the presence of non-hemopoietic cells or tissue having a mutated oncogene or other tumor-associated nucleic acid in the human.

In a preferred embodiment, the methods of the invention are used as an aid in the diagnosis in a human of a neoplastic, pre-malignant or proliferative disease. In another preferred embodiment, the method is used to detect a predictive risk factor for a neoplastic disease or disease progression in a human. Additionally, the methods of the invention are preferably used to determine disease prognosis in a human. In other preferred embodiments, the methods of the invention are used to determine the need for additional diagnostic tests, or for treatment.

In one embodiment of the invention, the methods of the invention enable the identification, selection, and/or monitoring of patients for a cancer therapy. In one aspect of this embodiment, the cancer therapy is a pharmaceutical product that inhibits, blocks, or interferes with the tyrosine kinase pathway or with tyrosine kinase-associated receptors. In one aspect, the pharmaceutical product inhibits, blocks, or interferes with HER-2/neu, EGFR, c-Kit, Flt-3, c-Met or PDGFR.

Particularly preferred methods of the invention enable detection in blood of mutated DNA, wherein the mutation is an acquired (somatic) mutation, as may be optionally shown by demonstrating the absence of the mutation in normal cells from the human having the acquired mutation, such as in normal leukocytes or other normal tissue. The invention thus provides a method for determining an acquired predictive risk factor for a non-hematologic disease in a human without cancer, the method comprising the steps of purifying extracellular nucleic acid from blood or blood plasma or serum from a human without cancer to prepare extracted nucleic acid containing a mutated DNA or a mutated DNA fragment, and concurrently or sequentially enriching for the mutated DNA or its fragment, wherein the mutated DNA or its fragment is concentrated and/or isolated from the remaining extracted nucleic acid, and thereafter amplifying the enriched mutated DNA or its fragment, or alternatively amplifying a signal from the enriched mutated DNA or its fragment, and then detecting the product of the amplified mutated DNA or the product of its amplified fragment, or the amplified signal of the mutated DNA or the amplified signal of its fragment, whereby said detection determines a predictive risk factor for a non-hematologic disease. Further, and optionally, by demonstrating the absence of the mutated DNA in normal cells of the human, such as normal leukocytes or other normal tissue, in which it is therefore demonstrated that the mutation is not an inherited or inborn mutation, the predictive risk factor is shown to be an acquired predictive risk factor. In a preferred embodiment the mutated DNA includes but is not limited to either a mutated oncogene DNA, for example mutated K-ras, P53, or APC, or a DNA microsatellite alteration. In preferred embodiments the non-hematologic disease is either colorectal adenoma, cervical dysplasia, atypical squamous metaplasia of the lung, bronchial dysplasia, atypical hyperplasia of the breast, prostatic intraepithelial neoplasia, atypical endometrial hyperplasia, dysplastic nevi of the skin, or Barrett's esophagus. In another aspect of the invention methods are provided for determining an acquired predictive risk factor by determining the presence of hypermethylated DNA, including non-mutated hypermethylated DNA, wherein said hypermethylated DNA is not present in normal tissue in the patient.

Also provided as embodiments of the methods of the invention are methods additionally comprising the steps of determining the nucleic acid sequence of the DNA fragment of extracellular nucleic acid in the extracted nucleic acid fraction that is associated with neoplastic or proliferative disease, wherein the nucleic acid sequence of the DNA fragment comprises a mutated or variant allele of a nucleic acid associated with a neoplastic or proliferative disease.

In addition to the methods noted above, the invention provides methods for isolating extracellular tumor-derived or tumor-associated DNA from a non-cellular fraction of a blood sample. In these embodiments the method comprises the steps of purifying extracellular DNA from a non-cellular fraction of blood to prepare a preparation of extracted nucleic acid using an extraction method; enriching the extracted DNA fraction for the portion of the fraction that is associated with neoplastic, pre-malignant or proliferative disease, and cloning the DNA fragments comprising the enriched DNA fraction that is associated with neoplastic, pre-malignant or proliferative disease. Also provided in this aspect of the invention are recombinant genetic constructs comprising a nucleic acid fragment that is associated with a neoplastic, pre-malignant or proliferative disease or condition that is prepared using the methods of the invention. Ribonucleic acid transcribed from the recombinant genetic constructs of the invention are also provided, as well as protein produced from translation of said RNA, and methods for using the translated proteins and peptides of the invention as epitopes for the production of antibodies and vaccines. In one aspect of the invention, the non-cellular fraction of blood is plasma or serum.

The invention also provides a method for concentrating and/or isolating any extracellular tumor-associated DNA or its fragment present in plasma or serum from a human without cancer for which specific oligonucleotide hybridization primers are available, the method comprising the steps of purifying extracellular nucleic acid from blood of a human without cancer to prepare nucleic acid containing a tumor-associated DNA or a tumor-associated DNA fragment, and concurrently or sequentially hybridizing an oligonucleotide to the tumor-associated DNA or a tumor-associated DNA fragment to produce a hybridized product of tumor-associated DNA or its fragment, and separating the hybridized product of tumor-associated DNA or its fragment from the remaining non-hybridized nucleic acid, thereby concentrating and/or isolating the tumor-associated DNA or its fragment. The invention thus provides a method for enriching for a mutated oncogene allele in plasma or serum, including but not limited to mutated K-ras, P53, or APC, and enriching for a DNA having a microsatellite alteration. In a preferred embodiment, the signal from the specific nucleic acid fragments comprising the enriched nucleic acid fraction is amplified using methods known to those with skill in the art, for example, branched DNA signal amplification, and combinations or variations thereof. In a preferred embodiment, detection of specific DNA fragments is performed using a detection method selected from the group consisting of gel electrophoresis, immunological detection methods, nucleic acid hybridization using a specific, fluorescent- or chromogenically-labeled probe, Southern blot analysis, electrochemiluminescence, reverse dot blot detection, spectroscopy, mass spectroscopy, and high-performance liquid chromatography.

The invention further provides a method for detecting a mutation in the DNA present in blood or a blood fraction, i.e., plasma or serum, of a human having a disease or premalignant condition in whom the presence of the disease or premalignant condition is unrecognized, wherein the mutation is an acquired mutation of known association with the disease or premalignant condition, and wherein the disease or premalignant condition includes but is not limited to colorectal adenoma, cervical dysplasia, atypical squamous metaplasia of the lung, bronchial dysplasia, atypical hyperplasia of the breast, prostatic intraepithelial neoplasia, atypical endometrial hyperplasia, dysplastic nevi of the skin, or Barrett's esophagus, wherein the method comprises the steps of purifying extracellular nucleic acid from blood or a blood fraction from a human in whom the presence of a disease or premalignant condition is unrecognized to prepare extracted nucleic acid containing a mutated DNA or its fragment wherein the mutation is of known association with the disease or premalignant condition, and amplifying the mutated DNA or its fragment, or alternatively amplifying a signal from the mutated DNA or its fragment, and detecting the product of the amplified mutated DNA or its fragment, or the amplified signal of the mutated DNA or its fragment. In a particularly preferred embodiment, the method enables the evaluation of blood or a blood fraction from a human for the mutated oncogene to assist in the identification of the premalignant disease or premalignant condition.

It is therefore the object of this invention to detect or infer the presence of cancerous or precancerous cells from non-hematologic premalignancies, within a human or animal body having a recognized neoplastic or proliferative disease or in those not previously diagnosed, by examining the plasma or serum fraction of blood for extracellular mutated DNA or tumor-derived or associated extracellular non-mutated DNA, using a nucleic acid detection assay.

Another object of this invention is to enable extraction of extracellular tumor-associated nucleic acid from plasma or serum in an enriching manner, wherein the tumor-associated nucleic acid is concentrated and/or isolated from the remaining extracted nucleic acid.

An advantageous application of this invention is to identify, either quantitatively or qualitatively, acquired mutant oncogenes or acquired tumor-associated DNA in the blood plasma or serum of humans or animals as to classify such patients for their risk of neoplastic disease.

Another advantageous application of this invention is to identify, either quantitatively or qualitatively, mutant oncogenes or tumor-associated DNA in the blood plasma or serum of humans or animals who are receiving therapies or who could receive a therapy, including but not limited to surgery including polypectomy, chemotherapy, radiotherapy, biotherapy including with monoclonal antibodies or cancer vaccines, iRNA-based therapy, anti-sense therapy, radionucleotide therapy, anti-angiogenic therapy, chemopreventive therapy and target-directed therapy such as those targeting receptor tyrosine kinase, as a guide to whether adequate therapeutic effect has been achieved or whether additional or more advanced therapy is required, and to assess prognosis in these patients, or to select a patient for the therapy.

Another advantageous application of this invention is to identify, either quantitatively or qualitatively, mutant oncogenes or tumor-associated DNA in the blood plasma or serum of humans or animals as to determine the need for additional diagnostic testing, wherein additional diagnostic testing includes but is not limited to endoscopy, colonoscopy, sigmoidoscopy, bronchoscopy, radiologic imaging, radionucleotide scanning, ultrasonography, PET scanning, or further evaluation of organ or site specific bodily fluids or stool, wherein bodily fluid includes but is not limited to that collected by drainage, aspiration, direct sampling, and lavage.

Another advantageous application of this invention is to identify, either by detection or inference, the presence of premalignant neoplasms, conditions, or diseases, through detection of acquired mutant oncogenes or acquired tumor-associated DNA in the blood of humans or animals in whom the presence of the neoplasm, condition, or disease is unrecognized, wherein the acquired mutant DNA derives from premalignant growths such as dysplasias or adenomas, or from other cells bearing an acquired mutated DNA of known association with a premalignant disease or condition, wherein said diseases and conditions include but are not limited to colorectal adenoma, cervical dysplasia, atypical squamous metaplasia of the lung, bronchial dysplasia, atypical hyperplasia of the breast, prostatic intraepithelial neoplasia, atypical endometrial hyperplasia, dysplastic nevi of the skin, and Barrett's esophagus. In addition, the invention advantageously provides a panel of several tumor-associated DNA that can distinguish malignant from premalignant conditions, or assist in medical monitoring to detect transformation of the growth to an outright malignancy, or to detect regression. Furthermore, the invention advantageously provides a means to define risk of malignancy in a human wherein the risk was previously unrecognized.

Advantageous application of the invention is provided as example but not limitation to include detection of mutated K-ras allele in blood from a human with adenoma; detection of mutated P53 allele in blood from a human with adenoma; detection of mutated APC allele in blood from a human with a colorectal cancer; detection of mutated K-ras allele in blood from a human with a proliferative disease; and detection of mutated K-ras allele in blood from a human with an in-situ (non-invasive or pre-invasive) carcinoma.

Thus, the invention provides a method of screening both healthy individuals and individuals at risk for cancer and premalignant conditions.

Another advantageous application of this invention is to identify, either quantitatively or qualitatively, one or more of multiple mutant oncogenes or other tumor-associated DNAs in the blood plasma or serum of humans or animals with or without cancer or not known to have cancer by use of a panel of oligonucleotide primers each specific for one of multiple differing tumor-associated alleles detected by the panel, wherein a particularly preferred application employs a nucleic acid enrichment method, and wherein the tumor-associated alleles are detected concurrently or sequentially. Additionally, said panel enables the inference of the presence of specific tumor types based upon mutated oncogenes or other tumor-associated mutated DNA detected by the panel. Additionally, said panel enhances identification of humans at risk for neoplastic disease. Additionally, said panel enhances identification of humans having premalignant or malignant tissue. A particularly preferred advantageous application of this invention identifies one or more of either K-ras, P53, and/or APC mutated alleles in blood from a human without cancer by use of a panel of primers specific for at least one or more of either K-ras, P53, or APC mutated alleles, whereby a human at risk for a gastrointestinal neoplastic disease is identified. In one aspect, said panel facilitates evaluation of a combination of tumor-associated DNA, wherein at least one DNA species is an oncogene DNA and at least one DNA is hypermethylated DNA. In another aspect, said panel facilitates evaluation of a combination of tumor-associated DNA, wherein at least one species is a translocated DNA. In another aspect, said panel facilitates evaluation of a combination of tumor-associated DNA, wherein at least one species is a receptor tyrosine kinase DNA. In another aspect, said panel facilitates evaluation of a combination of tumor-associated DNA, wherein at least one species is a hormone receptor DNA.

Specific preferred embodiments of the present invention will become evident from the following more detailed description of certain preferred embodiments and the claims.

DETAILED DESCRIPTION OF THE INVENTION

This invention provides methods for detecting or inferring the presence of cancerous and/or precancerous cells in a human or animal. The method comprises preparation of nucleic acid from plasma or serum wherein the extraction of nucleic acid may be performed with or without DNA precipitation or other separation of soluble nucleic acid from the plasma or serum, and further optionally performed using a method of enriching the tumor-associated DNA, wherein the tumor-associated DNA is concentrated and/or isolated, in either case followed by detection of the tumor-associated DNA preferentially following amplification of the tumor-associated DNA or a DNA fragment thereof or its signal. Enrichment of the mutated nucleic acid may occur prior to or during amplification by methods provided, including methods using an endonuclease or by methods involving hybridization of a mutated nucleic acid. Embodiments of the invention which provide for enrichment of mutated DNA from blood or blood fractions offer the beneficial advantage of enhancing detection of the mutated DNA. Direct sequencing of tumor-associated DNA is further made possible so that a broad range of tumor-associated DNA including mutated oncogenes and tumor suppressor genes, translocated genes, hypermethylated genes, microsatellite alterations in DNA, and other non-coding DNA related to the development of malignancy may be identified.

The invention further provides a number of methods of identifying mutations without prior knowledge of their location to be employed. This significantly increases the utility of detecting mutated DNA in plasma or serum, since genes such as APC and p53 exhibit point mutations throughout their coding regions (Hollstein et al., 1994, Nucleic Acids Res. 22: 3551-5). This is a significant improvement over the prior art, which requires prior knowledge of the location of a mutation or restriction of a search for mutants to the few most frequently mutated loci (“hot spots”; see Sorenson et al., 1993, Id.; Vasioukhin et al., 1994, Id.; Nawroz et al., 1996, Id.; Sorenson et al., 1994, Cancer Epidemiology, Biomarkers & Prevention 13: 67-71). Thus, a larger variety of malignant and premalignant conditions may be assessed (since different tumor types seem to carry particular mutations not found in other tumor types) and they may be detected for more thoroughly. It is to be noted and understood that the methods of DNA preparation and enrichment described herein are furthermore applicable to the previously described aspects of the invention utilizing amplification as well as methods of detection without amplification.

The invention provides methods for detection of an acquired (somatic) DNA alteration in the blood of a human without cancer, wherein normal cells from the human lack the alteration; thereby the invention provides for a method of determining acquired predictive risk factors for acquired diseases and conditions.

Moreover, the assays and methods of the invention can be performed qualitatively, whereby the amount of the DNA product produced is at least sufficient for efficient detection of the product, or quantitatively, whereby the amount of the DNA product produced is measured with reference to a standard useful in determining the significance of the amount of produced DNA product (for example, wherein the amount of DNA product is related to a disease state or risk of developing a disease state).

Specifically, the invention provides methods for detecting DNA in plasma or serum of a human or animal wherein the nucleic acid is associated with the existence of malignant or pre-malignant cells or tissues in the human or animal, thereby providing a method of detecting, evaluating, or monitoring neoplastic disease and premalignant conditions, or a sensitive predictive risk factor for neoplastic disease and premalignant conditions, wherein such diseases and conditions include but are not limited to premalignant diseases and conditions such as colorectal adenoma, cervical dysplasia, cervical intraepithelial neoplasia (CIN), atypical squamous metaplasia of the lung, bronchial dysplasia and metaplasia, atypical hyperplasia of the breast, ductal carcinoma in-situ, prostatic intraepithelial neoplasia (PIN), atypical endometrial hyperplasia, dysplastic nevi of the skin, Barrett's esophagus, myelodysplastic syndrome and preleukemia, myeloproliferative disorders including polycythemia vera and myelofibrosis, primary thrombocythemia and malignant diseases such as cancers of the breast, ovary, lung (including non-small cell lung cancer and small cell lung cancer), bronchial, pleural, colorectal, liver, gallbladder and biliary ducts, cervix, gastric, pancreas, bladder, uterus (including endometrial), brain, kidney, skin (including malignant melanoma), esophagus, head & neck, thyroid, sarcomas, cancers of unknown primary, and hematological malignancies such as acute leukemia (including acute myelogenous leukemia (AML), acute lymphocytic leukemis (ALL) and subtypes), chronic leukemia (including chronic myelogenous leukemia (CML) and chronic lymphocytic leukemia (CLL)), lymphoma (including Non-Hodgkins lymphoma and Hodgkins lymphoma), and multiple myeloma and other plasma cell and lymphoplasmacytic neoplasms.

The invention further provides methods for identification of humans having unrecognized disease who might therefore benefit from additional diagnostic testing, including but not limited to colonoscopy, sigmoidoscopy, endoscopy, bronchoscopy, radiologic imaging including CT scans, spiral CT scans, MRI, contrast studies, and plain films, ultrasonography, radionucleotide imaging, PET scanning, and evaluation of organ specific bodily fluid, stool, or lavage fluid, wherein bodily fluid includes but is not limited to that collected by drainage, aspiration, direct sampling, and lavage.

The invention particularly provides methods of detecting tumor-associated DNA that are receptor tyrosine kinase DNA and hormone receptor DNA, the further provides methods to thereby select patients for receptor tyrosine kinase-directed therapy or hormone-directed therapy, and to further monitor patients on said therapies.

A General Overview of the Inventive Methods

In the practice of the invention blood is drawn by standard methods into a collection tube either without anticoagulant for preparation of serum or with EDTA, heparin, or similar anticoagulants, most preferably EDTA, for preparation of plasma.

Plasma may optionally be subsequently converted to serum by incubation of the anticoagulated plasma with an equal volume of 0.025 molar calcium chloride at 37 degrees C. for a brief period, most preferably for 1-3 minutes, until clotting takes place. The clot may then be pelleted by a centrifugation, for example but not limitation at 1,000×g or greater, and the deproteinized plasma removed to another tube. In one preferred method, the volume of plasma used is 5 microliters mixed with 5 microliters of calcium chloride, then diluted to 100 microliters with water. Alternatively, the centrifugation may be omitted. The serum or plasma may be utilized directly for identification of mutant DNA. In one preferred embodiment, 10 microliters of serum or the prepared plasma is heated to a temperature greater than 90 degrees C., most preferably greater than 94 degrees C., for several minutes, most preferably 10. This heated substrate may then be cooled to below room temperature for a period of several minutes, or may be used directly in subsequent steps of the invention. In either instance an optional step of brief centrifugation, for example but not limitation at 1,000×g or greater may be performed to pellet any precipitate. Alternatively, heating may take place by placing a volume of sample, preferably 5 microliters, in a tube or microtiter well under mineral oil and heating in a microwave for greater than 3 minutes, more preferably 3-10 minutes (as described in Sandford et al., 1997, Biotechniques 23: 890-2). In most preferred embodiments, nucleic acid is extracted from plasma or serum as an initial step of the invention. The extraction step may be performed either prior to or concurrent with the enrichment step.

Gelatin Extraction Method:

In a preferred embodiment, DNA is co-precipitated from plasma or serum with gelatin by a method modified from that of Fournie et al. (1986, Anal. Biochem. 158: 250-256). A stock 5% (w/v) gelatin solution is prepared by mixing 1 gram gelatin (G8-500, Fisher, Pittsburgh, Pa.) with 20 mL sterile, double-distilled water, autoclaving for 30 minutes, and filtering through a 0.2 micron filter. The resultant solution is sequentially frozen in a dry ice/ethanol bath and thawed at room temperature for a total of five cycles. A working 0.3% gelatin solution is prepared by heating the stock solution to 60° C. and mixing 600 microliters of 5% gelatin with 25 microliters of 1 M Tris-HCl (pH 8.0) and 9.4 mL of sterile, double-distilled water.

Plasma or serum (160 microliters) is mixed with 12.8 microliters of 0.5 M EDTA and 467 microliters of sterile, double-distilled water, then emulsified for 3 minutes with 320 microliters of phenol or phenol:chloroform:isoamyl alcohol (25:24:1 ratio). The solution is centrifuged at 14,000×g for 10 minutes, and 570 microliters of the aqueous layer is removed to a clean tube. DNA is precipitated by addition of 142 microliters of the 0.3% gelatin working solution and of 500 microliters of cold absolute ethanol, followed by incubation at −20′C for 1-2 hours. Extracellular DNA may be precipitated within less than 1 h of incubation at −20° C., and a very short incubation may be preferable in some circumstances. Alternatively, longer incubation at −20° C. for 1-2 hours insures the precipitation of most DNA. The sample is centrifuged at 14,000×g at 4-6° C. for 15 minutes, washed once with cold 70% ethanol, and dried in a 60° C. heat block for 10 minutes. DNA is then recovered by the addition of 35 to 70 microliters of sterile, double-distilled water preheated to 60° C.

Glass Bead, Silica Particle, or Diatom Extraction Method.

As an alternative rapid method of extracting extracellular DNA from plasma or serum, glass beads, silica particles, or diatoms may be used, as in the method or adaptation of Boom et al. (Boom et al., 1991, J. Clin. Microbiol. 29: 1804-1811; Boom et al., 1989, J. Clin. Microbiol. 28: 495-503). Size fractionated silica particles are prepared by suspending 60 grams of silicon dioxide (SiO₂, Sigma Chemical Co., St. Louis, Mo.) in 500 mL of demineralized sterile double-distilled water. The suspension is then settled for 24 hours at room temperature. Four-hundred thirty (430) mL of supernatant is removed by suction and the particles are resuspended in demineralized, sterile double-distilled water added to a final volume of 500 mL. After an additional 5 hours of settlement, 440 mL of the supernatant is removed by suction, and 600 microliters of HCl (32% wt/vol) is added to adjust the suspension to a pH 2. The suspension is aliquotted and stored in the dark.

Lysis buffer is prepared by dissolving 120 grams of guanidine thiocyanate (GuSCN, Fluka Chemical, Buchs, Switzerland) into 100 mL of 0.1 M Tris hydrochloride (Tris-HCI) (pH 6.4), and 22 mL of 0.2 M EDTA, adjusted to pH 8.0 with NaOH, and 2.6 grams of Triton X-100 (Packard Instrument Co., Downers Grove, Ill.). The solution is then homogenized.

Washing buffer is prepared by dissolving 120 grams of guanidine thiocyanate (GuSCN) into 100 mL of 0.1 M Tris-HCl (pH 6.4).

Fifty microliters of plasma or serum are mixed with 40 microliters of silica suspension prepared as above, and with 900 microliters of lysis buffer, prepared as above, using an Eppendorf 5432 mixer over 10 minutes at room temperature. The mixture is then centrifuged at 12,000×g for one minute and the supernatant aspirated and discarded. The silica-DNA pellet is then washed twice with 450 microliters of washing buffer, prepared as above. The pellet is then washed twice with one mL of 70% (vol/vol) ethanol. The pellet is then given a final wash with one mL of acetone and dried on a heat block at 56 degrees centigrade for ten minutes. The sample is eluted for ten minutes at 56 degrees centigrade with a TE buffer consisting of 10 mM Tris-HCl, 1 mM EDTA (pH 8.0) with or without Proteinase K (100 ng/mL) as described by Boom et al. Following elution, the sample is then centrifuged at 12,000×g for three minutes, and the DNA-containing supernatant recovered (Boom et al., 1991, ibid.; Boom et al., 1989, ibid.; Cheung et al., 1994, J. Clin. Microbiol. 32: 2593-2597).

Acid Guanidinium Thiocyanate-Phenol-Chloroform Extraction Method.

As an alternative method, extracellular DNA may be extracted from plasma or serum in step one using variations of the acid guanidinium thiocyanate-phenol-chloroform extraction method. For example, extracellular DNA may be extracted from plasma or serum using TRI reagent, a monophase guanidine-thiocyanate-phenol solution, as described by Chomczynski (1993, Biotechniques 15: 532-534). One mL of plasma or serum is processed using 5-10 mL of TRI Reagent (TRI Reagent, Molecular Research Center, Cincinnati, Ohio, Trisolv, BioTecx Laboratories, Houston, Tex., TRIzol, GIBCO BRL/Life Technologies, Gaithersburg, Md., ISOGEN, Nippon Gene, Toyama, Japan, RNA Stat 60, Tel-test, Friendsword, Tex.) according to manufacturer's directions. DNA is precipitated from the interphase with ethanol.

Other commercially available kits known to the art may be utilized to extract nucleic acid from plasma or serum providing purified DNA for use in the invention's first step, including Qiagen columns (QIAamp blood kit, Qiagen, Basel, Switzerland), Boehringer Mannheim's High-Pure Viral Nucleic Acid kit, and other commercial kits for extraction of nucleic acid from plasma or serum as described herein, which are provided as example and not as limitation. Such kits may be used according to manufacturer's directions.

Enrichment Methods

Extracellular nucleic acid can be enriched from plasma, serum or whole blood using hybridization methods specific for particular species on extracellular nucleic acid. For example, nucleic acid derived from mutant K-ras oncogene DNA can be enriched from whole blood, serum or plasma using specific oligonucleotides for hybridization. Such oligonucleotides, generally ranging in size from about 12 to about 15 nucleotides or longer, are advantageously centered around the mutated nucleotide of interest to provide the greatest degree of discrimination between mutant and wildtype alleles. In particular, for the K-ras oncogene, the nucleotides of interest are the first and second positions of codons 12, 13 and 61. For K-ras, codon 12, first position, exemplary oligonucleotides have the sequence:

(SEQ ID No.: 1) GTTGGAGCTCGTGGCGTAG (SEQ ID No.: 2) GTTGGAGCTTGTGGCGTAG and (SEQ ID No.: 3) GTTGGAGCTAGTGGCGTAG, where the underlined nucleotide in each oligonucleotide is mutated from the wildtype.

In another example, the tumor suppressor gene p53, many mutations associated with the development of malignancy have been identified from a number of different tumors and tumor types. In colorectal carcinoma, for example, the most common mutation involves codon 175. For this mutation, exemplary enrichment oligonucleotides include the following:

(SEQ ID No.: 4) CCATGAGCACTGCTCAG (SEQ ID No.: 5) CCATGAGCTCTGCTCAG and (SEQ ID No.: 6) CCATGAGCCCTGCTCAG, where the underlined nucleotide in each oligonucleotide is mutated from the wildtype.

It will be apparent to one of ordinary skill in the art that any DNA point mutation can be enriched using oligonucleotides specific for the mutation and prepared to encompass the mutated site.

Additionally, enrichment oligonucleotides can be prepared to enrich for a particular gene such as an oncogene regardless of the presence of a mutation by preparing an oligonucleotide specific for the gene that does not encompass a site known to be involved in mutation related to the development of malignancy. Using such enrichment strategies, mutated nucleic acid is subsequently identified in the detection step of the methods of the invention, using mutation-specific oligonucleotides in hybridization assays, for example, or during a selective amplification step. For K-ras, enrichment oligonucleotides for nucleic acids encoding regions other than those containing codons 12, 13 or 61 are used to enrich a plasma, serum or whole blood sample for K-ras encoding nucleic acid sequences, both mutant and wildtype. Differentiation between mutant and wildtype fragment is then accomplished using detection methods such as allele-specific oligonucleotide hybridization assays.

Advantageously, more than one enrichment oligonucleotide species can be used simultaneously or sequentially. A panel of such enrichment oligonucleotides could include oligonucleotides specific for different mutated sites in a particular oncogene, or several mutated oncogenes in a multiplex enrichment assay. Differential detection methods, such as hybridization with distinguishable detectable labels, are then used to detect the different mutated nucleic acids resulting from the enrichment step of the methods of the invention.

Additional enrichment oligonucleotides include those oligonucleotides disclosed in co-owned U.S. Pat. No. 6,156,504, the disclosure of which is explicitly incorporated herein.

Additional Nucleic Acid Extraction Methods

Alternate means of purification which may be used to obtain DNA from serum or plasma, including selective retention on a size exclusion column or similar matrix, salting-out method, and other guanidinium thiocyanate extraction methods known in the art, including but not limited to all methods described in co-owned U.S. Pat. No. 6,156,504.

Alternatively, the plasma or serum may be prepared as described above, and one or several regions of DNA of interest may be enriched. This may be performed by hybridization of nucleic acid in the heated plasma or serum solution or of extracted nucleic acid against a manufactured strand of nucleic acid that is complementary to the sequence of interest (an affinity capture approach; see Seeger et al., 1997, Biotechniques 23: 512-7). Such “capturing” nucleic acids may consist of oligonucleotides, DNA or RNA constructs, or peptide nucleic acids. The capture of the target DNA serves as a means of enriching the target at the expense of other, non-hybridizing DNA that would otherwise compete with the target DNA during subsequent detection. The enrichment procedure occurs by hybridization at a low temperature under nonstringent conditions (see generally, Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual. (2nd ed.) Cold Spring Harbor Laboratory Press, New York), followed by washing of the target-capture complex to remove unbound, competing DNA. The capture nucleic acid may be bound to a surface, such as the wall of a tube or a nylon or other membrane, for example but not limitation on a microarray, or it may be bound to glass, magnetic or other beads that are incubated with the serum or plasma (Gelsthorpe et al., 1997, Biotechniques 22:1080-2; Rudi et al., 1997, Biotechniques 22: 506-11), thereby enabling separation of the mutated nucleic acid alleles from wild-type nucleic acid alleles, for example but not limitation, by using a magnetic or electric field, or by other methods well known to the art. A single region of interest may be examined in each sample, or several regions may be enriched for. By judicious choice of capturing nucleic acids, more than one target DNA may be captured simultaneously. It is obvious to one skilled in the art that this multiplexing approach will speed analysis of samples, and may be performed in a relatively tumor-specific fashion, i.e., with a set of capture probes that is mutated frequently in one type of tumor and infrequently in others. As an example, the genes TP53, KRAS, DCC and APC are often mutated in colorectal cancers and colorectal adenomas (precancerous tumors), while VHL and WT1 are more often mutated in renal cell carcinomas. Thus, the identification of mutations in a series of genes or tumor-associated DNA may, beyond identifying the presence of a malignancy or premalignancy in a patient, serve to identify the particular type of neoplasia by the particular set of genes or tumor-associated DNAs mutated or predict for the location of the neoplasia. Additionally, methods involving enrichment of the target nucleic acid may be performed on unprocessed plasma, serum or whole blood.

Alternatively, other means of enriching for the tumor-associated DNA of interest in a plasma or serum sample may be used. For example, antibodies directed against any portion of the target DNA may serve to capture it, with subsequent identification of the presence or absence of mutations. However, several antibodies may be needed to capture the entire gene or DNA of interest if this is desired, since DNA in plasma or serum often circulates in relatively small pieces, on the order of several hundred base pairs in length. Such capturing antibodies may be raised in animals by immunization with the target DNA or fragments thereof, or may be purified from naturally occurring anti-DNA antibodies found in humans with rheumatologic conditions. As explained above, the capturing antibodies may be bound to tubes or wells as in an ELISA, or may be bound to tubing through which a sample travels prior to further analysis, as by gas chromatography/mass spectroscopy or high performance liquid chromatography or bound to beads. These means and methods are provided by way of example and are not intended to be limiting.

Following the preparation of plasma or serum as described above, and preferably following an amplification step, a detection step for mutations in oncogenes or other tumor-associated DNA is performed. It is the detection of mutants that indicates the presence of one or more mutant-bearing cells within the patient. Moreover, as explained above, the pattern of mutants may be relatively specific for certain types of proliferative diseases. It bears stressing that this invention, comprising either precipitation of extracellular DNA from serum or plasma or preparation of serum, plasma or whole blood or other bodily fluid for analysis without precipitation of DNA followed by detection of mutations (including, but not limited to, point mutation, insertion, deletion and translocation) may be applied to detection of malignant neoplasms and detection of precursor, premalignant conditions.

A tumor-associated DNA detected in blood plasma or serum of a human may be further characterized as being an acquired (somatic) DNA alteration by demonstrating the absence of the alteration in normal cells of the human using methods known in the art consisting of extraction of the DNA from normal cells, and amplifying for the altered DNA of interest in a manner as to enable detection, wherein an absence of the altered DNA in normal cells from the human indicates the alteration detected within blood plasma or serum DNA to be an acquired DNA alteration, and not an inherited or inborn DNA alteration.

Detection of DNA sequence mutants may proceed by any of a number of methods known to those skilled in the art (Kilger et al., 1997, Nucleic Acids Res. 25: 2032-4). The sequence may be detected directly by nucleic acid sequencing methods such as cycle sequencing (Sarkar et al., 1995, Nucleic Acids Res. 23: 1269-70) or direct dideoxynucleotide sequencing, in which some or all of the enriched DNA of interest that has been harvested from plasma or serum is used as a template for sequencing reactions. An oligonucleotide primer or set of primers specific to the gene or DNA of interest is used in standard sequencing reactions.

Other methods of DNA sequencing, such as sequencing by hybridization, sequencing using a “chip” containing many oligonucleotides for hybridization (as, for example, those produced by Affymetrix Corp.; Ramsay et al., 1998, Nature Biotechnology 16: 40-44; Marshall et al., 1998, Nature Biotechnology 16: 27-31), sequencing by HPLC (DeDionisio et al., 1996, J. Chromatogr A 735: 191-208), and modifications of DNA sequencing strategies such as multiplex allele-specific diagnostic assay (MASDA; Shuber et al., 1997, Hum. Molec. Genet. 6: 337-47), dideoxy fingerprinting (Sarkar et al., 1992, Genomics 13: 441-3; Blaszyk et al., 1995, Biotechniques 18: 256-60; Martincic et al., 1996, Oncogene 13: 2039-44), and fluorogenic probe-based PCR methods (such as Taqman; Perkin-Elmer Corp.; Heid et al., 1996, Genome Res. 6: 986-94) and cleavase-based methods may be used. Alternatively, approaches that detect specific mutations of interest such as allele-specific amplification or restriction digest methods such as CARD (as disclosed in co-owned U.S. Pat. No. 6,156,504, incorporated by reference) may be used singly or in combination to identify extracellular mutant DNA (Zafiropoulos et al., 1997, Biotechniques 23:1104-1109). It is clear to one skilled in the art that a variety of suitable methods for determining alterations at the DNA sequence level would suffice for this step of the invention, and the methods mentioned here are not intended to be comprehensive or limiting, but merely to serve as examples.

Methods that detect mutations in DNA without precisely identifying the mutated base or bases are also able to be used in this invention, inclusive of those methods of detection previously described in the application. Single strand conformation polymorphism (SSCP) analysis, for example, can identify variations from normal in a region of DNA without precisely defining the mutated base(s)(Orita et al., 1989, Proc. Natl. Acad. Sci. USA 86: 2766-70; Suzuki et al., 1990, Oncogene 5:1037-43). Similarly, heteroduplex analysis (Glavac et al., 1995, Hum. Mutat. 6 (4): 281-7), denaturing gradient gel electrophoresis (Pellegata et al., 1992, Anticancer Res. 12:1731-1736) and mismatch cleavage assays can identify a patient carrying a DNA mutation by analysis of extracted or unextracted plasma or serum DNA. All of these procedures require cleavage of the sample DNA with restriction endonucleases, or alternatively amplification by PCR or a similar amplification technique, to obtain uniform sized DNA fragments for gel electrophoresis analysis.

Detection of the target tumor-associated DNA can also be accomplished by means of signal amplification techniques. For example, the branched DNA assay (Chiron) uses a specific DNA probe to a target DNA (in this case, any of the tumor-associated DNA of interest) to identify the presence of the target (Urdea et al., 1993, AIDS 7: S11-4). The signal is amplified by means of modifications made to the probe which allow many fluorescent detector molecules (also DNA) to hybridize. However, any signal amplification method may be used in the invention. Similarly, oligonucleotide ligation assays may be used to amplify and detect the mutation of interest from amplified or directly processed serum or plasma DNA (Benson et al., 1996, Thromb. Res. 83: 87-96).

For the purposes of this invention, tumor-derived or associated DNA includes but is not limited to:

-   -   DNA related to mutated oncogenes or other mutated DNA, a partial         list of which includes H-ras, K-ras, N-ras, c-myc, fms, src,         fos, sis, jun, bcl-2, or VHL (Von Hippel-Lindau gene), and DNA         microsatellite alterations; DNA related to tumor suppressor         genes, a partial list of which includes p53, RB, MCC, APC, DCC,         NF1, WT 1; and hypermethylated DNA.         It is particularly to be noted that tumor-associated DNA         includes, but is not limited to:     -   receptor tyrosine kinase-associated DNA, including but not         limited to HER-2/neu DNA, epidermal growth factor receptor DNA         (EGFR DNA), c-kit DNA, c-Met DNA, Flt-3 DNA, and         platelet-derived growth factor receptors (PDGFR) DNA; JAK-2 DNA,         including JAK-2 V617F mutated DNA; tumor DNA that is a hormone         receptor DNA, including but not limited to estrogen receptor         DNA, progesterone receptor RNA, insulin and insulin-like growth         factor-1 receptor DNA including IGF-I DNA and IGFR-1 DNA, and         guanylyl cyclase C (GCC) receptor DNA; and translocated DNA         including inversions and fusion gene DNA, wherein said         tumor-associated DNA include but are not limited to bcl-2/IgH         DNA, bcl-1/IgH DNA, bcr-ab1 DNA, PML/RAR DNA, AML1-ETO DNA,         EWS/FLI-1 DNA, EWS/ERG DNA, ETS family gene fusion DNA,         TMPRSS2/ERG DNA, TMPRSS2-ETV1 DNA, TEL-AML1, TMPRSS2-ETV4 DNA,         C15orf21/ETS DNA, HNRPA2B VETS DNA, RET fusion gene DNA, NTRK1         fusion gene DNA, PAX8-PPARG DNA, MECT1-MAML2 DNA, ETV6-NTRK3         DNA, NPM-ALK DNA, EML4-ALK DNA, TPM3-ALK DNA, TFG-ALK DNA,         ATIC-ALK DNA, PAX3-FKHR DNA, PAX7-FKHR DNA, ETV6-PDGFRB DNA,         EWSR1-DDIT3 DNA, FUS-DDIT3 DNA, PCM1-JAK2 DNA, BCR-JAK2 DNA         SS18-SSX DNA and JAZF1-JJAZ1 DNA.         It is to be understood that methods of detection and/or         enrichment for extracellular tumor-associated DNA from blood or         blood fractions including non-cellular blood fractions such as         plasma and serum, as described herein by the invention may         similarly be applied as methods for detection and/or enrichment         of extracellular tumor-associated DNA present in other bodily         fluids, including particularly ascitic fluid, pleural effusions,         urine, saliva, cerebrospinal fluid, pericardial effusions,         sputum and bronchial secretions, breast fluid including         secretion from the ducts and nipple of the breast, gastric         secretions, and fluid aspirated or drained from cystic or         semi-cystic tissues, wherein evaluation of the bodily fluid         offers distinct diagnostic advantage in humans in whom the         presence of a disease is unknown.

Methods of Enrichment Using an Endonuclease.

Enrichment of the target or mutated nucleic acid, whereby the concentration of the target nucleic acid is increased with respect to wild-type or non-mutated nucleic acid, may be accomplished by using an endonuclease either before or during an amplification step, as disclosed in co-owned U.S. Pat. No. 6,156,504, the disclosure of which is explicitly incorporated herein. In preferred embodiments, the endonuclease is selected from the group consisting of but not limited to BstNI, HinP I, and Msp I.

Therapeutic Applications

The extraction of extracellular DNA from plasma or serum permits further analysis or other manipulation of that DNA, from which further clinical utility is realized. In this optional step of the invention, extracellular DNA is analyzed to define the characteristics or composition of the tumor from which the DNA originates. Any of several methods may be used, dependent upon the desired information, including nucleic acid sequencing, spectroscopy including proton NMR spectroscopy, biochemical analysis, and immunologic analysis. In the preferred embodiment, such nucleic acid is cloned into a plasmid vector, for example the pGEM-T vector plasmid (Promega) and sequenced using a commercial kit such as Sequenase 2.0 (USB). Analysis to define the characteristics or composition of the extracellular nucleic acid, and thus the characteristics of the originating tissue, affords a wide array of clinical utility, including the description, characterization, or classification of the tumor, whether known or occult, such as by tissue of origin, by type (such as premalignant or malignant), phenotype, and genotype, and by description or characterization of tumor behavior, physiology and biochemistry, as to gain understanding of tumor invasiveness, propensity to metastasize, and sensitivity or resistance to various therapies, thereby allowing the prediction of response to either ongoing or planned therapy and, further, allowing evaluation of prognosis. Comparison of the characteristics of extracellular DNA to previous biopsy or surgical specimens permits further evaluation of tumor heterogeneity or similarity in comparison to that specimen, and thus evaluation of tumor recurrence.

The methods of the invention are particularly useful to select patients or monitor the response of patients to cancer therapies that are directed to specific protein or nucleic acid targets or enzymatic pathways. In particular, the invention enables selection and monitoring of patients for receptor tyrosine kinase-directed therapies such as tyrosine kinase inhibitor (or antagonist) therapies. Examples of such therapies include but are not limited to cetuximab, trastuzumab, imatinib mesylate, and sunitinib. In particular, a patient is selected for a tyrosine kinase inhibitor therapy when the presence, amount, concentration, or level of a receptor tyrosine kinase DNA in the patient's plasma or serum, said DNA correlating to the receptor target of the therapy, is greater than the presence, amount, concentration, or level of said receptor tyrosine kinase DNA in the plasma or serum of a reference group that is not a candidate for the therapy, such reference group being humans without cancer or without disease, and/or being humans with cancer or disease but without abnormal expression of receptor tyrosine kinase DNA. Similarly, a patient is selected for a receptor tyrosine kinase inhibitor therapy when the presence, amount, concentration, or level of a receptor tyrosine kinase DNA correlating to the receptor target of the therapy in a patient's plasma or serum is comparable to the presence, amount, concentration, or level of a receptor tyrosine kinase DNA in plasma or serum of a reference group of humans with cancer or with disease who are judged to be acceptable candidates for the receptor tyrosine kinase inhibitor therapy. A human may be serially monitored for response to a receptor tyrosine kinase inhibitor therapy by qualitatively or quantitatively comparing the presence, amount, concentration, or level of a receptor tyrosine kinase DNA in the human's plasma or serum over serial time points.

Following extraction of extracellular DNA from plasma or serum, complimentary ribonucleic acid (RNA) may be transcribed or manufactured from the DNA. In a preferred embodiment, transcription of RNA is performed by employing a primer with an RNA polymerase promoter region joined to the standard primer sequence for the DNA of interest. RNA complimentary to the DNA is then transcribed from the attached promoter region. In an alternative method, extracellular nucleic acid is cloned into an expression vector, and RNA complimentary to the DNA is transcribed. Furthermore, as an optional preferred embodiment, the complimentary RNA is used in an in vitro translation reaction to manufacture tumor-associated or tumor-specific protein.

Extraction of extracellular nucleic acid from blood serum or plasma, and characterization, transcription of complimentary RNA, and translation to tumor-associated or tumor-specific protein, provides significant utility, both in the delineation of those who might benefit from therapy, including chemoprevention or assignment of therapy, and in the development of tumor-specific therapies. Sequencing of extracellular nucleic acid or transcription of complementary RNA allows assignment or development of antisense compounds, including synthetic oligonucleotides and other antisense constructs appropriately specific to the extracellular DNA, such as by construction of an expression plasmid such as by adapting the method of Aoki et al. (1995, Cancer Res. 55: 3810-3816). Similarly, defining tumor characteristics allows assignment of specific monoclonal antibody or vaccine therapies appropriately specific to the extracellular DNA, including receptor tyrosine kinase inhibitor therapies. Production of corresponding immunologic protein can be used in the development of tumor-specific monoclonal antibodies. Similarly, translated protein can be used in tumor-specific vaccine development. Furthermore, the extracellular DNA permits a means of defining or allowing the construction of a DNA construct which may be used in vaccine therapy.

Of particular value, the invention allows the development and application of these tumor-specific therapies even when only premalignant tumors, early cancers, or occult cancers are present. Thus, the invention allows therapeutic intervention when tumor burden is low, immunologic function is relatively intact, and the patient is not compromised, all increasing the potential for cure.

The invention also provides methods for transcribing RNA complementary to the isolated extracellular nucleic acid from plasma or serum, as well as methods for producing peptides and proteins (or fragments thereof) encoded thereby. Additional methods for using the peptide and proteins as antigens for producing antibodies specific for the peptides and proteins encoded by the extracellular nucleic acids of the invention are also provided. The isolated extracellular nucleic acids of the invention are also used in methods for producing antisense oligonucleotides, either synthetically or using recombinant genetic methods, and the use thereof for affecting gene expression in a cell will be appreciated by one having ordinary skill in the art in view of the methods for isolating and identifying said extracellular nucleic acid provided herein. Vaccine production, as is understood by one with skill in the art, is also enabled using the methods of the invention.

The methods of the invention and preferred uses for the methods of the invention are more fully illustrated in the following Examples. These Examples illustrate certain aspects of the above-described method and advantageous results. These Examples are shown by way of illustration and not by way of limitation.

Example 1 Detection of Mutated K-Ras DNA in the Plasma of Patients without Cancer Using an Endonuclease-Based Enrichment Method

Colorectal adenoma are common premalignant neoplasms associated with a risk for development of colorectal cancer. Blood plasma was prospectively obtained from 25 individuals who had K-ras mutated colorectal adenoma. None of the individuals were known to have cancer, nor did colonoscopy or other testing demonstrate cancer in any individual. Five to ten milliliters of blood was collected from each individual, and plasma was fractionated from the whole blood by centrifugation at 400×g at room temperature for ten minutes. Extracellular DNA was then extracted from the plasma using a gelatin precipitation method as previously described. The extracted plasma DNA was amplified with a polymerase chain reaction assay which enriched for mutated K-ras by employing simultaneous restriction digestion and PCR amplification by utilizing a BstNI restriction endonuclease, the method of which (CARD) is described in full in co-owned U.S. Pat. No. 6,156,504, the disclosure of which is explicitly incorporated herein. Mutations in the final digested amplified product were identified by agarose gel electrophoresis, and further prior to final enzyme digestion by identification of altered bases using dot blot hybridization, wherein following amplification five microliters of product were applied to a nylon membrane (MSI, Westboro, Mass.). Replicate blots were hybridized to ³²P-radiolabelled oligonucleotides designed to identify point mutations in positions 1 and 2 of codons 12 of the K-ras gene (Mutaprobe Human K-ras 12 set, Oncogene Science, Uniondale, N.Y.). Hybridization and wash conditions were as specified by the membrane's manufacturer. Blots were exposed to x-ray film for 10 hours at −80 degrees C. Mutated K-ras DNA was detected in the plasma of 20 individuals. Sequence analysis demonstrated that the altered base mutation found in the adenoma was similarly demonstrable in the plasma of the individuals.

This example demonstrates that an enrichment-based assay enables detection of mutated nucleic acid in individuals without cancer; further enables detection of the presence of premalignant tissue including colorectal adenoma; further enables identification of a predictive risk factor; further enables sequence identification of the mutated DNA in blood and further predicts for the sequence of the mutated DNA in tissue.

Example 2 Detection of Mutated P53 DNA in the Plasma of Individuals without Cancer Using an Enrichment Assay

P53 mutations are common oncogene mutations in both malignant and premalignant tumors. Plasma was obtained prospectively from individuals undergoing colonoscopy and assayed for plasma DNA P53 mutations at codons 175 and 248. Five to ten milliliters of blood were collected in EDTA-coated siliconized glass vacutainer tubes from each individual assayed. Plasma was fractionated from whole blood by centrifugation at 400×g at room temperature for ten minutes. Extracellular DNA was then extracted from plasma using a gelatin precipitation extraction as previously described. Seven microliters of the gelatin-precipitated DNA were then used in an amplification reaction in which P53 DNA was enriched using a restriction endonuclease. Oligonucleotide primers were designed to perform a hemi-nested amplification of a portion of exon 5 for codon 175, wherein the first primer (P53-1) is 5′-GCAGTCACAGCACATGACG-3′; the second primer (P53-2) is 5′-AATCAGAGGCCTGGGGAC-3′; and the third primer (P53-3) is 5′-GGGCCAGACCTAAGAGCAAT-3′. A reaction mixture consisting of lx Taq polymerase (Fisher, Pittsburgh, Pa.) in a volume of 50 microliters was prepared. This mixture was amplified by polymerase chain reaction under mineral oil for 20 cycles with denaturation at 94 degrees C. for 1 minute, annealing at 58 degrees C. for 90 seconds, and extension at 72 degrees C. for 90 seconds. This was followed by a CARD step of combined amplification and restriction digestion, in which 5 microliters of the initial amplification product was transferred to a new reaction mix identical to the K-ras mixture previously described for CARD in co-pending and co-owned U.S. Ser. No. 08/818,058, the disclosure of which is explicitly incorporated herein, except for the use of 10 picomoles each of primers P53-1 and P53-2 in place of K-ras primers, and the substitution of 8 units of restriction enzyme HinP1 I (New England BioLabs, Beverly, Mass.) for BstNI. Cycling parameters were as for the CARD K-ras amplification. A final digestion with HinP1 I was performed prior to identification of mutants by agarose gel electrophoresis. To detect codon 248 P53 mutations a similar CARD assay was performed using primers (P53-4): 5′-TTGGGCCGGTGTTATCTC-3′; and (P53-5): 5′-ATGGTGCGGATGGGCCTC-3′, designed to amplify a portion of exon 7. Mutations at codon 248 were enriched and amplified in the same manner as described above for codon 175, except substituting HinP1 I with Msp I (New England BioLabs, Beverly, Mass.). Mutations in the final digested amplified product were identified by agarose gel electrophoresis.

Extracellular mutated P53 DNA was demonstrated in the plasma of 3 individuals, none of whom had cancer, including one individual having a codon 175 P53 mutation, and 2 individuals having a codon 248 P53 mutation. Colonoscopy demonstrated a premalignant lesion (an adenoma) in each of two of these individuals, and a proliferative disease (a hyperplastic polyp) in the third individual.

This example further demonstrates that extracellular mutated nucleic acid can be detected in the blood of humans without cancer; further that enrichment of the target nucleic acid may be accomplished using a restriction endonuclease; further that mutated P53 DNA may be detected in the blood of humans without cancer; further that mutated P53 DNA may be enriched from the blood of humans without cancer; further that mutated P53 DNA may be detected in the blood of individuals with premalignant neoplasms or proliferative disease; further that P53 DNA provides a predictive risk factor for neoplastic disease. While the example demonstrates detection of P53 mutations at codon 175 and 248, P53 mutations at other codons may similarly be detected in blood by substituting the appropriate primers and restriction enzyme.

Example 3 Enhanced Identification of Humans with Premalignant Neoplasms Using a Multiplex Assay or Assay Panel Targeting Differing Mutated Oncogenes

Since individuals with premalignant neoplasms and conditions may harbor differing mutated oncogenes or differing DNA microsatellite alterations, evaluating blood for a number of differing mutated oncogenes or tumor-associated nucleic acids are thereby more likely to enable identification of those individuals harboring neoplasms, thereby increasing overall sensitivity in identification of said individuals. To provide example but not limitation for this approach, plasma was evaluated by a panel of assays which detect mutated K-ras DNA (by the method provided in example 1), and mutated P53 DNA (by the method provided in example 2). Plasma from individuals without cancer shown to harbor colorectal adenoma were evaluated for both extracellular mutated K-ras and mutated P53 DNA. Mutated K-ras but not P53 DNA was demonstrated in the plasma from 20 individuals having K-ras mutated adenoma. However, mutated P53 but not K-ras DNA was additionally demonstrated in the plasma from 2 individuals having wild-type ras adenoma. Together, the panel of both K-ras and P53 assays thereby enabled increased identification of individuals with colorectal adenoma. Increasing the number of mutated oncogenes and tumor-associated nucleic acids detected by the assay array or panel (for example but not limitation by including an APC assay as provided in example 4) thereby increases the ability to identify individuals harboring premalignant neoplasms, thereby increasing the utility of the assay.

Example 4 Detection of an APC Gene Mutation in Plasma from an Individual with a Colorectal Neoplasm

APC gene mutations are common mutations in colorectal premalignant and malignant neoplasms. Example 4 describes herein detection of mutated APC DNA in blood:

APC mutations may be demonstrated in blood or tissue by the method as follows: Three overlapping sets of oligonucleotide primers are prepared to the mutation cluster region in exon 15 of the APC gene, which are estimated to account for over 60% of all APC mutations in colorectal neoplasms. The primer sequences are:

APC-1, 5′-TCCACACCTTCATCTAATGCC-3′; APC-2, 5′-CATTCCACTGCATGGTTCAC-3′; APC-3, 5′-CTGAAGATCCTGTGAGCGAA-3′; APC-4, 5′-TCAGGCTGGATGAACAAGAA-3′; APC-5, 5′-CTTCGCTCACAGGATCTTCA-3′; APC-6, 5′-TTTGAGAGTCGTTCGATTGC-3′.

DNA extracted from plasma, serum, whole blood, or tissue is subjected to polymerase chain reaction amplification with 1 picomole each of either primers APC-1 and APC-2, or primers APC-3 and APC-4 for 25 cycles at a denaturing temperature of 94 degrees C. for 60 seconds, annealing at 51 degrees C. for 90 seconds, and extension at 72 degrees C. for 90 seconds each cycle. The reaction mixture consists of 1× Taq buffer, 1.5 mM MgCl₂, 200 micromolar dNTPs, and 1 unit Taq polymerase (Fisher, Pittsburgh, Pa.) in a volume of 50 microliters. Hemi-nested PCR amplification is then performed on 5 microliters of the first amplification product, wherein primers APC-1 and APC-2 are replaced with primers APC-1 and APC-5; and in a separate reaction primers APC-1 and APC-2 replaced with primers APC-2 and APC-3; and in a separate reaction primers APC-3 and APC-4 replaced with primers APC-6 and APC-4. Reaction conditions for the second round of amplification are the same as for the first, except that 10 picomoles of each primer are used, and the cycle number is 35. The PCR products are detected by agarose gel electrophoresis, bands are excised from the gel and DNA isolated using the GeneClean kit (Bio101) according to the manufacturer's instructions. DNA is then asymmetrically reamplified with one primer at 100 picomoles and the other at 2 picomoles for eventual cycle sequencing, wherein primer pairs are: APC-1 and APC-5; APC-2 and APC-3; APC-4 and APC-6. The asymmetric amplification is performed as described in the art (McCabe, 1990, PCR Protocols. A guide to methods and applications (Innis, Gelfand, Sninsky, & White, eds.) Academic Press, pp. 76-83) using approximately 1.4 nanograms of each PCR product and annealing at 51 degrees C. Cycle sequencing is then performed as described in the art (Brow, 1990, PCR Protocols. A guide to methods and applications (Innis, Gelfand, Sninsky, & White, eds.) Academic Press, pp. 189-196) using the limiting primer labeled with ³²P.

In Example 4 provided herein, five to ten millimeters of blood was collected in an EDTA-coated siliconized glass vacutainer tube from an individual with colorectal cancer whose tumor was known to harbor an APC mutation consisting of a five base deletion at 3961-3965. Plasma was fractionated from whole blood by centrifugation at 400×g at room temperature for ten minutes. DNA was then extracted from 200 microliters of plasma using the High-Pure Viral Nucleic Acid kit (Boehringer Mannheim). The extracted DNA was initially amplified as described above using primers APC-1 and APC-7 (5′-TGCTGGATTTGGTTCTAGGG-3′), then reamplified with primers APC-7 and APC-8 (5′-TCAGACGACACAGGAAGCAG-3′) as in the hemi-nested reactions described above. The PCR products were electrophoresed through a 5% agarose gel and examined by ethidium bromide staining. The appropriate region of the gel was excised and prepped by the GeneClean, and this DNA then cycle sequenced as described above, thereby confirming an APC mutation in the plasma DNA.

Plasma from this individual having APC mutated plasma DNA was further evaluated for the presence of mutated K-ras DNA (by the method described in example 1), and mutated P53 DNA (by the method described in example 2). Plasma was negative for both mutated K-ras and mutated P53 DNA in this individual.

This example demonstrates that mutated APC DNA may be detected in blood. Further, detection of mutated APC in blood is indicative of the presence of mutated tissue, and provides a predictive risk factor for neoplastic disease. The example demonstrates that detection of mutated APC in blood is particularly advantageous in predicting for neoplastic disease of a gastrointestinal origin, and particularly a colorectal neoplastic disease. It will be understood that enriching the extracted DNA for APC by methods as described in the invention will further increase the sensitivity of the assay for detection of mutated APC DNA in blood. It is further shown by this example that it is particularly advantageous to include methods detecting mutated APC within a multiplexed assay or an oncogene or tumor-associated nucleic acid assay panel or array, wherein it is particularly advantageous to assay blood plasma or serum for mutated APC in addition to mutated K-ras and/or mutated P53. It is well recognized that APC mutations occur early and commonly in premalignant neoplasms such as colorectal adenoma, thus it is particularly evident that it is advantageous to detect mutated APC in the blood of humans without cancer, as to predict for premalignant disease or risk for neoplastic disease, and to further indicate the need for additional diagnostic testing including but not limited to endoscopy, colonoscopy, sigmoidoscopy, radiologic imaging, radionucleotide scanning, ultrasonography, PET scanning, or further evaluation of organ or site specific bodily fluids or stool, wherein bodily fluid includes but is not limited to that collected by drainage, aspiration, direct sampling, and lavage.

Example 5 Detection of Mutated K-Ras DNA in the Plasma of a Human without Cancer Having a Hyperplastic Proliferative Condition

Hyperplastic colorectal polyps are non-neoplastic proliferative conditions. Blood was prospectively examined from a human found upon colonoscopy and polypectomy to have a K-ras mutated hyperplastic polyp but not to have cancer. The method of examination was identical to the method provided in example 1. Mutated K-ras DNA was similarly demonstrated in the plasma from the human. This example demonstrates that the methods of the invention enable detection of mutated DNA in the blood of individuals having hyperplastic tissue harboring mutated DNA.

Example 6 Detection of Mutated K-Ras DNA in the Plasma of a Human with an In-Situ (Non-Invasive) Carcinoma

In-situ carcinomas are early cancers which by definition are localized and non-invasive. A human undergoing a colonoscopy was found to have a K-ras mutated in-situ colorectal carcinoma. Plasma was prospectively obtained from the human and examined using the methods identical to those provided in example 1. Mutated K-ras DNA was similarly detected in the plasma from the human. This example demonstrates that the methods of the invention enable detection of mutated DNA in blood from humans having localized, non-invasive or pre-invasive, in-situ malignancy when the malignancy harbors mutated DNA.

Example 7 Prophetic Examples of the Use of the Assays of the Invention

The following example is illustrative of potential clinical uses for the assays of the invention.

Case 1

A 70 year old woman with a long history of cigarette smoking will visit her doctor because she is concerned about her risk of developing lung cancer. A sample of blood will be drawn and plasma will be prepared. An aliquot of the plasma will be incubated with metal beads containing oligonucleotides complementary to exons of the TP53 tumor suppressor gene bound to their surface. The beads will be drawn to the side of the tube with a magnet, and the tube will then be washed several times with water. The tube will then be heated to release the affinity-captured TP53 DNA fragments, and the solution containing these fragments will applied to a sequencing chip useful for detecting mutations in the TP53 gene. The machine designed to read the sequencing chip will detect a deletion of codon 158 of the TP53 gene. Confirmation of the presence of the TP53 mutation will thereafter be obtained from a sputum sample, and it will be concluded that the patient is at high risk for development of lung cancer. She will be closely followed by spiral CT scan, and bronchoscopy as indicated, and the patient will have blood plasma regularly monitored by a version of the invention adapted specifically for her TP53 mutation. After enrichment of the plasma for the exon carrying the codon 158 mutation using metal beads followed by amplification, a quantitative assay for the presence of the mutation will be used to determine the amount of mutant present in the plasma. For one year, this patient will have no detectable mutant DNA, followed by a steady rise in the amount of mutant DNA that will then be noted over six months. No clinical or radiographic evidence of disease would otherwise be present at this time in this case. The patient might begin a P53-directed chemopreventive therapy and after a successful course remain free of disease while being monitored by the codon 158 assay.

This example further illustrates the use of the invention in a quantitative fashion, in this case using the affinity-capture version of the invention. A tumor suppressor gene frequently altered in lung cancer (TP53) is enriched from the plasma and used as the substrate for a quantitative portion of the invention. This mutant can then be followed and intervention begun early, when chemopreventive therapy is most effective.

Case 2

In this hypothetical case, a 42 year old woman will be diagnosed with breast cancer. Upon pathology, an ELISA followed by FISH test of her tumor will demonstrate that it is a HER-2/neu negative tumor. The woman will be treated with standard adjuvant chemotherapy without receiving adjuvant trastuzumab (Herceptin), a receptor tyrosine kinase inhibitor monoclonal antibody. Three years after completing adjuvant chemotherapy the woman will develop a recurrence of her breast cancer, in this case recurring as metastatic breast cancer to the bone. It is recognized in the art that some patients who have their primary breast cancer testing negative for HER-2/neu, will later show a HER-2/neu positive tumor upon retesting of their metastatic cancer. These patients will thus become potential candidates for trastuzumab therapy, even if they were not candidates initially. In this hypothetical case the woman will be re-evaluated for HER-2/neu positivity using the methods of the invention. The woman will give a blood specimen, and plasma will be separated from the specimen, and DNA will be extracted from the plasma specimen using the inventive methods as previously described. A portion of the extracted DNA will then be quantitatively amplified using Taqman PCR using primers specific for HER-2/neu DNA. It will be shown that the woman has HER-2/neu DNA levels in her plasma greater than expected for a woman without cancer, and further levels greater than expected for a woman with a HER-2/neu negative cancer, and further that the levels are consistent with the woman having HER-2/neu positive cancer. Based upon these results of the inventive method, the woman will then be selected for and receive trastuzumab therapy. The woman will further be monitored for her response to trastuzumab therapy by providing plasma specimens on a serial basis, and HER-2/neu DNA levels will be assessed in a serial manner using the methods of the invention.

This example further illustrates the use of the invention to select and monitor patients for receptor tyrosine kinase-directed therapies, in this case being trastuzumab, a monoclonal antibody tyrosine kinase inhibitor. The invention in this case facilitates assessment of receptor tyrosine kinase status in a patient with cancer recurrence, where in this case the primary tumor was HER-2/neu negative.

These clinical vignettes are meant as examples of the uses to which the invention may be put, and are not meant in any way to be limitations upon the range or type of assays or extracellular mutant DNAs detectable in the plasma or serum by the invention.

It should be understood that the foregoing disclosure emphasizes certain specific embodiments of the invention and that all modifications or alternatives equivalent thereto are within the spirit and scope of the invention as set forth in the appended claims. 

1. A method of detecting DNA of a gene translocation or fusion in the plasma or serum of a human, wherein said gene translocation or fusion is an ALK gene translocation or fusion, the method comprising the steps of: a) extracting DNA from the plasma or serum of a human; b) assaying a portion of the extracted DNA for DNA of a translocation or fusion of the ALK gene; and c) detecting DNA corresponding to said translocation or fusion of the ALK gene, or an amplified product thereof.
 2. The method of claim 1, wherein step b) comprises amplifying said extracted DNA for an ALK gene translocation or fusion.
 3. The method of claim 1, wherein the DNA of an ALK gene translocation or fusion is one selected from the group comprising NPM-ALK DNA, EML4-ALK DNA, TPM3-ALK DNA, TFG-ALK DNA, and ATIC-ALK DNA.
 4. The method of claim 1, wherein the ALK gene translocation is associated with a cancer in said human.
 5. A method of evaluating the plasma or serum of a human for DNA of a gene translocation or fusion, wherein said translocation or fusion is an ALK gene translocation or fusion, the method comprising the steps of: a) extracting DNA from plasma or serum of a human; b) assaying a portion of the extracted DNA for an ALK gene translocation or fusion; and c) detecting for DNA corresponding to sn ALK gene translocation or fusion, whereby plasma or serum of a human is thereby evaluated for DNA of a gene translocation or fusion.
 6. The method of claim 5, wherein step b) comprises amplifying said extracted DNA for an ALK gene translocation or fusion.
 7. The method of claim 5, wherein the DNA of an ALK gene translocation or fusion is one selected from the group comprising NPM-ALK DNA, EML4-ALK DNA, TPM3-ALK DNA, TFG-ALK DNA, and ATIC-ALK DNA.
 8. The method of claim 5, wherein the ALK gene translocation is associated with a cancer in said human. 